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as explained in my comments on the PR
This test started to fail on Sage 10.3.beta2
…with SAGE_SPKG_INST set by sage-spkg
added 28 commits
December 25, 2023 23:43
<!-- ^^^^^ Please provide a concise, informative and self-explanatory title. Don't put issue numbers in there, do this in the PR body below. For example, instead of "Fixes #1234" use "Introduce new method to calculate 1+1" --> <!-- Describe your changes here in detail --> <!-- Why is this change required? What problem does it solve? --> <!-- If this PR resolves an open issue, please link to it here. For example "Fixes #12345". --> <!-- If your change requires a documentation PR, please link it appropriately. --> The following link `L` is ambient isotopic to the treefoil knot but has one additional loop.  ``` sage: L = Link([[1, 7, 2, 6], [3, 1, 4, 8], [5, 5, 6, 4], [7, 3, 8, 2]]) sage: L.regions()` [[-5], [8, 4, 6, 2], [7, -2], [3, -8], [1, -6, 5, -4], [-1, -3, -7]] sage: L.seifert_circles() [[5], [1, 7, 3], [2, 8, 4, 6]] ``` Invoking `L.braid()` does not terminate. The problem already occurs on the first application of a Vogel move which leads to an extended `pd_code = [[10, 7, 2, 6], [3, 1, 4, 8], [11, 5, 6, 4], [7, 3, 8, 2], [12, 9, 5, 1], [11, 9, 12, 10]]`. A diagram of the corresponding link looks like this:  The labels `C1`, `C2 = [3, 1, 4, 8]`, `D = [11, 9, 12, 10]` and `E = [12, 9, 5, 1]` correspond to the variables in the code and the numbers to the edges. In case of `C1`the correct list of edges would be `[5, 11, 6, 4]` but the code produces `[11, 5, 6, 4]`. This is caused by usage of the `index` method of the `list` class which always returns the first occurrence of a value in the list, i.e. by the line: ``` C2[C2.index(b)] = newedge + 2 ``` To fix it I replace the method by a local function: ``` def idx(cross, edge): r""" Return the index of an edge in a crossing taking loops into account. A loop appears as an edge which occurs twice in the crossing. In all cases the second occurrence is the correct one needed in the Vogel algorithm. """ i = cross.index(edge) if cross.count(edge) > 1: return cross.index(edge, i+1) else: return i ``` > In all cases the second occurrence is the correct one needed in the Vogel algorithm. The according argumentation goes as follows: If the loop is clockwise oriented the edge has a positive sign in the region, else a negative sign. In the first case the outgoing side of the edge always occurs after the incoming one in the PD-code (edge 1 in the first picture below and edge 2 in the second). In the second case the incoming side of the edge always occurs after the outgoing one in the PD-code (edge 2 in the first picture below and edge 1 in the second).   Thus, this corresponds to the fact that in the first case `a` and `b` leave the crossings `C1` and `C2` (in the original link) whereas they arrive there in the second case. Another way to fix the issue would be to remove all loops from the diagram before starting the Vogel algorithm. But this would harm regular isotopy which might violate the expectation of the user. Thus, I implement this as an optional feature. This gives the user the possibility to obtain a braid of smaller index if he is fine with ambient isotopy. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> <!-- If your change requires a documentation PR, please link it appropriately --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> <!-- Feel free to remove irrelevant items. --> - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [ ] I have linked a relevant issue or discussion. - [x] I have created tests covering the changes. - [x] I have updated the documentation accordingly. ### ⌛ Dependencies <!-- List all open PRs that this PR logically depends on - #12345: short description why this is a dependency - #34567: ... --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> URL: #36884 Reported by: Sebastian Oehms Reviewer(s): Sebastian Oehms, Travis Scrimshaw
…pendent) wheels
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We simplify the Sage distribution by installing more Python packages as
platform-independent wheels.
- No longer use direct installation using the deprecated `setup.py
install`
- `pip` bootstraps itself from its wheel
- `setuptools` is installed as a wheel
- remove the 2nd copy of setuptools (SPKG `setuptools_wheel`)
We also add the build backends `hatchling` and `flit_core` to
`PYTHON_TOOLCHAIN`. This fixes some missing dependencies, including
`editables` (as reported in https://groups.google.com/g/sage-
release/c/uP-rwlM__MU/m/oU-49z9VAwAJ).
The package `deprecation` is no longer used by any package (has it been
... deprecated?) and is removed here.
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- Depends on #36888 (for fixing the html workflow)
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URL: #36885
Reported by: Matthias Köppe
Reviewer(s): Dima Pasechnik
…categories
Adding a few links on errors in the doc
Also fixing a few ruff UP details
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URL: #36897
Reported by: Frédéric Chapoton
Reviewer(s): David Coudert
this was scripted using `ruff --fix --select=UP009,UP018,UP034,UP039,UP025 src/sage/combinat` see https://docs.astral.sh/ruff/rules/#pyupgrade-up ### 📝 Checklist - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. URL: #36898 Reported by: Frédéric Chapoton Reviewer(s): David Coudert
<!-- ^^^^^ Please provide a concise, informative and self-explanatory title. Don't put issue numbers in there, do this in the PR body below. For example, instead of "Fixes #1234" use "Introduce new method to calculate 1+1" --> <!-- Describe your changes here in detail --> The new release adds support for FLINT 3. https://github.com/flatsurf/e-antic/releases/tag/2.0.0 Thanks @saraedum for preparing this release! <!-- Why is this change required? What problem does it solve? --> <!-- If this PR resolves an open issue, please link to it here. For example "Fixes #12345". --> <!-- If your change requires a documentation PR, please link it appropriately. --> ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> <!-- If your change requires a documentation PR, please link it appropriately --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> <!-- Feel free to remove irrelevant items. --> - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [ ] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies <!-- List all open PRs that this PR logically depends on - #12345: short description why this is a dependency - #34567: ... --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> URL: #36901 Reported by: Matthias Köppe Reviewer(s): Travis Scrimshaw
Use more block-scope tags to avoid doctest warnings like
```
File "src/sage/libs/coxeter3/coxeter.pyx", line 1198, in
sage.libs.coxeter3.coxeter.CoxGroupIterator.__next__
Warning: Consider using a block-scoped tag by inserting the line 'sage:
# optional - coxeter3' just before this line to avoid repeating the tag
4 times
from sage.libs.coxeter3.coxeter import get_CoxGroup as CoxGroup,
CoxGroupIterator # optional - coxeter3
```
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URL: #36902
Reported by: David Coudert
Reviewer(s): Matthias Köppe
This is fixing a few ruff details (code UP) and adding some links to
errors in the doc, in the `geometry` folder.
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URL: #36903
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
…rization
Use more block-scope tags to avoid doctest warnings like
```
File "src/sage/game_theory/normal_form_game.py", line 1093, in
sage.game_theory.normal_form_game.NormalFormGame._gambit_
Warning: Consider using a block-scoped tag by inserting the line 'sage:
# optional - gambit' just before this line to avoid repeating the tag 29
times
threegame = NormalFormGame() # optional - gambit
```
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URL: #36904
Reported by: David Coudert
Reviewer(s): Matthias Köppe
…arious doctest warnings
We fix the following warnings
```
File "src/sage/categories/finite_complex_reflection_groups.py", line
558, in sage.categories.finite_complex_reflection_groups.FiniteComplexRe
flectionGroups.ParentMethods.milnor_fiber_poset
Warning: Consider using a block-scoped tag by inserting the line 'sage:
# optional - gap3' just before this line to avoid repeating the tag 4
times
W = ReflectionGroup(4) # optional - gap3
**********************************************************************
File "src/sage/categories/finite_complex_reflection_groups.py", line
565, in sage.categories.finite_complex_reflection_groups.FiniteComplexRe
flectionGroups.ParentMethods.milnor_fiber_poset
Warning: Consider using a block-scoped tag by inserting the line 'sage:
# optional - gap3' just before this line to avoid repeating the tag 6
times
W = ReflectionGroup([4,2,2]) # optional - gap3
File "src/sage/coding/ag_code_decoders.pyx", line 32, in
sage.coding.ag_code_decoders
Warning: Consider using a block-scoped tag by inserting the line 'sage:
# long time' just before this line to avoid repeating the tag 9 times
channel = channels.StaticErrorRateChannel(code.ambient_space(), tau)
# long time
File "src/sage/plot/graphics.py", line 1819, in
sage.plot.graphics.Graphics.show
Warning: Variable 'G' referenced here was set only in doctest marked '#
needs sage.symbolic'; '# long time, needs sage.symbolic'
G.show(scale='semilogy') #
long time
File "src/sage/quadratic_forms/ternary_qf.py", line 924, in
sage.quadratic_forms.ternary_qf.TernaryQF.find_p_neighbor_from_vec
Warning: Variable 'Q' referenced here was set only in doctest marked '#
needs sage.libs.pari'
Q.find_p_neighbor_from_vec(3, (0,0,1))
[315 tests, 0.38 s]
```
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URL: #36905
Reported by: David Coudert
Reviewer(s): Matthias Köppe
…etc)
this is fixing various minor details in `quadratic forms`
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URL: #36906
Reported by: Frédéric Chapoton
Reviewer(s): David Coudert
For the specific case of curves with $j=0$ and isogeny degree $\ell=3$, the `compute_isogeny_stark()` function sometimes fails to find an isogeny even though it exists. In this simple patch we increase the precision of the power-series arithmetic in `compute_isogeny_stark()` by one digit, which makes the computation succeed for this special case too. Fixes #21883. URL: #36909 Reported by: Lorenz Panny Reviewer(s):
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This is adding a few useful methods in the free pre-Lie algebras.
In particular, an approximate version of the preLie Baker-Campbell-
Hausdorff formula.
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URL: #36913
Reported by: Frédéric Chapoton
Reviewer(s): Travis Scrimshaw
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<!-- ^^^^^ Please provide a concise, informative and self-explanatory title. Don't put issue numbers in there, do this in the PR body below. For example, instead of "Fixes #1234" use "Introduce new method to calculate 1+1" --> <!-- Describe your changes here in detail --> Standard modularization changes: - Using more lazy imports, more specific imports and similar - Some try... except for imports of element implementations - `# needs` - incidental doctest cosmetics <!-- Why is this change required? What problem does it solve? --> <!-- If this PR resolves an open issue, please link to it here. For example "Fixes #12345". --> This is: - Cherry-picked from #35095 <!-- If your change requires a documentation PR, please link it appropriately. --> ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> <!-- If your change requires a documentation PR, please link it appropriately --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> <!-- Feel free to remove irrelevant items. --> - [x] The title is concise, informative, and self-explanatory. - [ ] The description explains in detail what this PR is about. - [ ] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies <!-- List all open PRs that this PR logically depends on - #12345: short description why this is a dependency - #34567: ... --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> URL: #36917 Reported by: Matthias Köppe Reviewer(s): David Coudert
There is one example of ring in the doc about coercion.
Currently not tested and very much using old-style.
So let's refresh it and test it.
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URL: #36919
Reported by: Frédéric Chapoton
Reviewer(s): Ruchit Jagodara
Nauty has a generator of k-trees. We add an interface to this generator. This is a complement of #36587. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> <!-- If your change requires a documentation PR, please link it appropriately --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> <!-- Feel free to remove irrelevant items. --> - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [x] I have created tests covering the changes. - [x] I have updated the documentation accordingly. ### ⌛ Dependencies <!-- List all open PRs that this PR logically depends on - #12345: short description why this is a dependency - #34567: ... --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> URL: #36924 Reported by: David Coudert Reviewer(s): Matthias Köppe
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fixing a few details in C-finite sequences
main change : use `Parent` (new coercion framework) instead of `Ring`
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URL: #36934
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
…doctest
Fixes #36931
as suggested by @orlitzky
Marked blocker so that the failure on fedora does not show up in CI.
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URL: #36935
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
a few minor details in the modified file
mainly to use `Parent` in some place in the doc
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URL: #36943
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
…pt` problems
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The new release 0.0.4 provides cysignals integration:
- milahu/gnumake-tokenpool#4
Fixes #36944
To verify that the tokenpool mechanism is being used:
```
$ DEBUG_JOBCLIENT=1 make ptest
```
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URL: #36948
Reported by: Matthias Köppe
Reviewer(s): John H. Palmieri
…on_count` doctest dataflow warnings
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Fixes #36920
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In part cherry picked from:
- #35095
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- Depends on #36905 (merged here)
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URL: #36950
Reported by: Matthias Köppe
Reviewer(s): David Coudert
Samurai is a C99 ninja implementation with an almost-compatible version scheme, except that it has only two version components instead of the three that ninja has. We update the "sed" call used to parse the version number out of `ninja --version` so that it can parse a samurai version too. This should only matter on systems where (for example) /usr/bin/ninja points to samurai. That's not typical, but it recently became possible to do on Gentoo in an "official" way. URL: #36955 Reported by: Michael Orlitzky Reviewer(s): Matthias Köppe
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